Xiongwu Wu

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc Chemoreceptors in Caulobacter crescentus: trimers of receptor dimers in a partially ordered hexagonally packed array
    Cezar M Khursigara
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    J Bacteriol 190:6805-10. 2008
  2. ncbi request reprint Isotropic periodic sum: a method for the calculation of long-range interactions
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MD 20892, USA
    J Chem Phys 122:44107. 2005
  3. pmc Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, MD 20892, USA
    J Struct Biol 183:429-40. 2013
  4. pmc Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 137:044106. 2012
  5. pmc Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 135:204101. 2011
  6. pmc Isotropic periodic sum of electrostatic interactions for polar systems
    Xiongwu Wu
    Laboratory of Computational Biology, NHLBI, NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 131:024107. 2009
  7. pmc Toward canonical ensemble distribution from self-guided Langevin dynamics simulation
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 134:134108. 2011
  8. ncbi request reprint Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation
    Xiongwu Wu
    Laboratory of Biophysical Chemistry, NHLBI, NIH, Building 50, Room 3308, Bethesda, Maryland 20892, USA
    J Am Chem Soc 124:5282-3. 2002
  9. pmc Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water
    Xiongwu Wu
    Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 86:1946-58. 2004
  10. ncbi request reprint A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy
    Xiongwu Wu
    Laboratory of Biophysical Chemistry, NHLBI, National Institutes of Health, Building 50, Room 3308, 50 South Drive, Bethesda, MD 20892, USA
    J Struct Biol 141:63-76. 2003

Collaborators

Detail Information

Publications29

  1. pmc Chemoreceptors in Caulobacter crescentus: trimers of receptor dimers in a partially ordered hexagonally packed array
    Cezar M Khursigara
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    J Bacteriol 190:6805-10. 2008
    ....
  2. ncbi request reprint Isotropic periodic sum: a method for the calculation of long-range interactions
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institute of Health, Bethesda, MD 20892, USA
    J Chem Phys 122:44107. 2005
    ..Therefore, this method provides a general approach to an efficient calculation of long-range interactions for various kinds of molecular systems...
  3. pmc Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, MD 20892, USA
    J Struct Biol 183:429-40. 2013
    ..Using several examples, we illustrate the application of this method in flexible fitting of atomic structures into density maps derived from cryo-electron microscopy. ..
  4. pmc Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 137:044106. 2012
    ..Especially for large systems, RXSGLD has remarkable advantages in terms of replica exchange efficiency, conformational searching ability, and system size extensiveness...
  5. pmc Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 135:204101. 2011
    ..For studies where preserving accessible conformational space is critical, such as free energy calculations and protein folding studies, SGLDfp is an efficient approach to search and sample the conformational space...
  6. pmc Isotropic periodic sum of electrostatic interactions for polar systems
    Xiongwu Wu
    Laboratory of Computational Biology, NHLBI, NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 131:024107. 2009
    ..For both homogeneous and heterogeneous systems, the 3D-IPS/discrete fast Fourier transform method using either the nonpolar or the polar electrostatic 3D-IPS potentials results in very similar simulation results...
  7. pmc Toward canonical ensemble distribution from self-guided Langevin dynamics simulation
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 134:134108. 2011
    ..This development makes SGLD not only an efficient approach for conformational searching, but also an accurate means for conformational sampling...
  8. ncbi request reprint Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation
    Xiongwu Wu
    Laboratory of Biophysical Chemistry, NHLBI, NIH, Building 50, Room 3308, Bethesda, Maryland 20892, USA
    J Am Chem Soc 124:5282-3. 2002
    ..Energetic analysis indicates that the driving force of the folding is the intrapeptide interaction, while the solvent interaction opposes the folding...
  9. pmc Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water
    Xiongwu Wu
    Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Biophys J 86:1946-58. 2004
    ..Comparing unfolding simulations using MD and SGMD methods demonstrate that SGMD simulations can qualitatively reproduce the kinetics of the peptide system...
  10. ncbi request reprint A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy
    Xiongwu Wu
    Laboratory of Biophysical Chemistry, NHLBI, National Institutes of Health, Building 50, Room 3308, 50 South Drive, Bethesda, MD 20892, USA
    J Struct Biol 141:63-76. 2003
    ....
  11. pmc Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems
    Xiongwu Wu
    Laboratory of Computational Biology, NHLBI, NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 129:154115. 2008
    ..Example simulations demonstrate that this method can accurately and efficiently calculate long-range interactions for molecular simulation...
  12. pmc Lateral density of receptor arrays in the membrane plane influences sensitivity of the E. coli chemotaxis response
    Cezar M Khursigara
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    EMBO J 30:1719-29. 2011
    ....
  13. doi request reprint Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex
    Jeffrey S Lengyel
    Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Structure 16:93-103. 2008
    ....
  14. pmc Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy
    Jacqueline L S Milne
    Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, MD 20892, USA
    J Biol Chem 281:4364-70. 2006
    ....
  15. pmc Maintain rigid structures in Verlet based cartesian molecular dynamics simulations
    Peng Tao
    Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Chem Phys 137:134110. 2012
    ..Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency...
  16. pmc Role of HAMP domains in chemotaxis signaling by bacterial chemoreceptors
    Cezar M Khursigara
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 105:16555-60. 2008
    ..Based on these results, we propose that the compact and expanded conformations represent the "kinase-on" and "kinase-off" states of chemoreceptor trimers, respectively...
  17. pmc Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine
    Jacqueline L S Milne
    Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
    EMBO J 21:5587-98. 2002
    ....
  18. ncbi request reprint Mutagenesis and modeling of the peroxiredoxin (Prx) complex with the NMR structure of ATP-bound human sulfiredoxin implicate aspartate 187 of Prx I as the catalytic residue in ATP hydrolysis
    Duck Yeon Lee
    Laboratory of Cell Signaling, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892 0301, USA
    Biochemistry 45:15301-9. 2006
    ..The modeling and mutagenesis analyses strongly implicate Asp187 of Prx I as the catalytic residue responsible for ATP hydrolysis in the cysteinesulfinic acid reduction of Prx by hSrx...
  19. pmc Accurate high-throughput structure mapping and prediction with transition metal ion FRET
    Xiaozhen Yu
    Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Structure 21:9-19. 2013
    ..Our results open the door to rapid, accurate mapping and prediction of protein structures at low concentrations, in large complex systems, and in living cells...
  20. pmc Molecular dynamics simulations of perylene and tetracene librations: comparison with femtosecond upconversion data
    Tilman Rosales
    Optical Spectroscopy Section, Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Building 10 Magnuson CC, 5D14, 10 Center Dr, Bethesda, Maryland 20892, USA
    J Phys Chem A 112:5593-7. 2008
    ..Sarkar, N.; Takeuchi, S.; Tahara, T. J. Phys. Chem. A 1999, 103, 4808]...
  21. ncbi request reprint Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method
    Jeffery B Klauda
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Phys Chem B 111:4393-400. 2007
    ....
  22. doi request reprint 2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor
    Alberto Bartesaghi
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Science 348:1147-51. 2015
    ....
  23. pmc A common molecular basis for exogenous and endogenous cannabinoid potentiation of glycine receptors
    Wei Xiong
    Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Neurosci 32:5200-8. 2012
    ..Such a specific interaction likely stems from a common molecular basis involving the S296 residue in the TM3 of the α1 and α3 subunits...
  24. pmc Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, 5635 Fishers Lane, Room T900, Bethesda, MD 20892 9314
    Adv Chem Phys 150:255-326. 2012
    ..Since these methods are direct and straightforward, they can be used in conjunction with many other sampling methods or free energy methods by simply replacing the integration of degrees of freedom that are normally sampled by MD or LD...
  25. ncbi request reprint Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland 20892, United States
    J Phys Chem B . 2016
    ....
  26. pmc Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor
    Xiongwu Wu
    Laboratory of Computational Biology, NHLBI, NIH, Bethesda, Maryland 20892, USA
    J Chem Phys 145:164110. 2016
    ....
  27. pmc Self-guided Langevin dynamics via generalized Langevin equation
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland, 20892
    J Comput Chem 37:595-601. 2016
    ..In particular, SGLD-GLE is fully size extensive and can be used in arbitrarily large systems, making it an appealing alternative to LD. © 2015 Wiley Periodicals, Inc. ..
  28. pmc A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water
    Xiongwu Wu
    Laboratory of Computational Biology, National Heart, Lung, and Blood Institute NHLBI, National Institutes of Health NIH, Bethesda, Maryland, United States of America
    PLoS Comput Biol 11:e1004480. 2015
    ..For one of the most challenging systems in constant pH calculation, SNase Δ+PHS/V66K, our VMMS simulation shows that it is the state-dependent water penetration that causes the large deviation in lysine66's pKa. ..
  29. pmc Maturation of the HIV-1 core by a non-diffusional phase transition
    Gabriel A Frank
    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Nat Commun 6:5854. 2015
    ..Our studies suggest that HIV maturation involves a non-diffusional phase transition in which the detaching layer of the cleaved CA lattice is gradually converted into a roll that ultimately forms the surface of the mature conical core. ..